U.S. patent number 10,612,088 [Application Number 14/774,648] was granted by the patent office on 2020-04-07 for massively multiplexed rna sequencing.
This patent grant is currently assigned to THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY. The grantee listed for this patent is THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY. Invention is credited to Mitchell Guttman, Eric S. Lander, Alexander A. Shishkin, Christine F. Surka.
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United States Patent |
10,612,088 |
Shishkin , et al. |
April 7, 2020 |
Massively multiplexed RNA sequencing
Abstract
A method for parallel sequencing target RNA from samples from
multiple sources while maintaining source identification is
provided. The method includes providing samples of RNA comprising
target RNA from two or more sources; labeling, at the 3' end, the
RNA from the two or more sources with a first nucleic acid adaptor
that comprises a nucleic acid sequence that differentiates between
the RNA from the two or more sources; reverse transcribing the two
or more sources to create a single stranded DNA comprising the
nucleic acid sequence that differentiates between the RNA from the
two or more sources; amplifying the single stranded DNA to create
DNA amplification products that comprise the nucleic acid sequence
that differentiates between the RNA from the two or more sources;
sequencing the DNA amplification products thereby parallel
sequencing target RNA from samples from multiple sources while
maintaining source identification.
Inventors: |
Shishkin; Alexander A.
(Pasadena, CA), Guttman; Mitchell (West Hollywood, CA),
Surka; Christine F. (Pasadena, CA), Lander; Eric S.
(Cambridge, MA) |
Applicant: |
Name |
City |
State |
Country |
Type |
THE BROAD INSTITUTE, INC.
MASSACHUSETTS INSTITUTE OF TECHNOLOGY |
Cambridge
Cambridge |
MA
MA |
US
US |
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Assignee: |
THE BROAD INSTITUTE, INC.
(Cambridge, MA)
MASSACHUSETTS INSTITUTE OF TECHNOLOGY (Cambridge,
MA)
|
Family
ID: |
51581131 |
Appl.
No.: |
14/774,648 |
Filed: |
March 14, 2014 |
PCT
Filed: |
March 14, 2014 |
PCT No.: |
PCT/US2014/027015 |
371(c)(1),(2),(4) Date: |
September 10, 2015 |
PCT
Pub. No.: |
WO2014/152155 |
PCT
Pub. Date: |
September 25, 2014 |
Prior Publication Data
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|
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Document
Identifier |
Publication Date |
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US 20160024572 A1 |
Jan 28, 2016 |
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Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
Issue Date |
|
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61786103 |
Mar 14, 2013 |
|
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12Q
1/6806 (20130101); C12Q 1/6874 (20130101); C12Q
1/6869 (20130101); C12Q 2535/122 (20130101); C12Q
2521/107 (20130101); C12Q 2563/179 (20130101) |
Current International
Class: |
C12P
19/34 (20060101); C12Q 1/6869 (20180101); C12Q
1/6874 (20180101); C12Q 1/6806 (20180101) |
Field of
Search: |
;435/91.2 |
References Cited
[Referenced By]
U.S. Patent Documents
Other References
International Search Report and Written Opinion dated Jul. 8, 2014
for PCT/US2014/027015, Jul. 8, 2014, 22 pages. cited by applicant
.
Prokaryia, ThermoPhage Single-Stranded DNA Ligase [online], Jun. 4,
2014, 3 pages. cited by applicant .
Van Nieuwerburg, "Quantitative Bias in Illumina TruSeq and a Novel
Post Amplification Barcoding Strategy for Multiplexed DNA and Small
RNA Deep Sequencing", PLoS One, vol. 6, No. 10, Oct. 2011, pp. 1-6.
cited by applicant .
International Preliminary Report on Patentability dated Sep. 24,
2015 for PCT/US2014/027015, Sep. 24, 2015, 7 pages. cited by
applicant.
|
Primary Examiner: Wilder; Cynthia B
Attorney, Agent or Firm: Johnson, Marcou, Isaacs & Nix,
LLC Nix, Esq.; F. Brent Rey, Patent Agent; Gertrund U.
Government Interests
STATEMENT OF GOVERNMENT SUPPORT
This invention was made with government support under grant number
1DP50D012190-01 awarded by the National Institutes of Health and
grant number 1P50HG006193-01 awarded by National Human Genome
Research Institute, National Institutes of Health. The government
has certain rights in the invention.
Parent Case Text
CROSS-REFERENCE TO RELATED APPLICATION
This application is the U.S. National Stage of International
Application No. PCT/US2014/027015, filed Mar. 14, 2014, published
in English under PCT Article 21(2), which claims the priority
benefit of the earlier filing date of U.S. Provisional Application
No. 61/786,103 filed Mar. 14, 2013, which is specifically
incorporated by reference herein in its entirety.
Claims
We claim:
1. A method for parallel sequencing target RNA from samples from
multiple sources while maintaining source identification,
comprising: providing samples of RNA comprising target RNA from two
or more sources; labeling, at the 3' end, the target RNA with a
first nucleic acid adaptor that is at least two nucleotides in
length and comprises a nucleic acid sequence that is indexed to the
origin or source of the sample and differentiates between the RNA
from the two or more sources; pooling the 3' labeled RNA; reverse
transcribing the 3' labeled RNA from the two or more sources to
create a single stranded DNA comprising the nucleic acid sequence
that differentiates between the RNA from the two or more sources;
amplifying the single stranded DNA to create DNA amplification
products that comprise the nucleic acid sequence that
differentiates between the RNA from the two or more sources;
sequencing the DNA amplification products; thereby parallel
sequencing target RNA from samples from multiple sources while
maintaining source identification.
2. The method of claim 1, further comprising labeling, at the 3'
end, the single stranded DNA with a second nucleic acid adaptor
that comprises a site for binding of a PCR primer wherein the
second nucleic acid adaptor optionally comprises a sequencing
adaptor and/or a second nucleic acid sequence that can
differentiate between single stranded DNA from two or more
sources.
3. The method of claim 1, wherein the first nucleic acid adaptor
comprises a sequencing adaptor.
4. The method of claim 3, further comprising pooling the single
stranded DNA with single stranded DNA from one or more additional
sources, wherein the single stranded DNA from the one or more
additional sources is similarly labeled.
5. The method of claim 1, further comprising depleting the samples
of non-target RNA.
6. The method of claim 5, wherein depleting the samples of
non-target RNA comprises using one or more probes that specifically
hybridize to the non-target RNA, wherein the one or more probes
comprise a label that facilitates removal of the probe from the
sample.
7. The method of claim 1, wherein the first nucleic acid adaptor is
3' end blocked and/or wherein the first nucleic acid adaptor
comprises RNA, DNA or a RNA-DNA hybrid.
8. The method of claim 2, wherein the second nucleic acid adaptor
is 3' end blocked and/or wherein the second nucleic acid adaptor
comprises RNA, DNA or a RNA-DNA hybrid.
9. The method of claim 2, wherein the nucleic acid sequence that
differentiates between the single stranded DNA from the two or more
sources is at least two nucleotides in length.
10. The method of claim 1, further comprising removing and/or
degrading the reverse transcription primers and/or removing and/or
degrading the RNA from the sample.
11. The method of claim 1, wherein the samples of different origins
comprise samples of the same cell type and/or tissue type exposed
to different environmental conditions.
12. The method of claim 11, wherein the different environmental
conditions are contacts with different test agents.
13. The method of claim 1, where the target RNA is mRNA, and
differences in expression of the mRNA are measured across samples
from different sources.
14. The method of claim 1, further comprising quantifying the
sequenced target RNAs of samples from multiple sources.
15. The method of claim 1, comprising sorting the sequenced target
RNAs to their respective sources.
16. The method of claim 1, further comprising labeling, at the 5'
end, the RNA from the two or more sources with a first nucleic acid
adaptor that comprises a nucleic acid sequence that differentiates
between the RNA from the two or more sources.
17. The method of claim 16, further comprising labeling, at the 5'
end, the single stranded DNA with a second nucleic acid adaptor
that comprises a site for binding of a PCR primer and/or a
sequencing adaptor.
Description
FIELD OF THE DISCLOSURE
This disclosure relates to RNA sequencing and specifically to
multiplex RNA sequencing and enhanced methods of the same.
BACKGROUND
Next-generation sequencing is rapidly becoming the method of choice
for the analysis of RNA, such as for transcriptional profiling. In
contrast to microarray technology, sequencing allows identification
of novel transcripts and does not require preexisting knowledge of
the sequence of the genome. In addition, unlike hybridization-based
detection, the sequencing of RNA allows genome-wide analysis of
transcription at single nucleotide resolution.
Despite progress, sequencing of specific strands of RNA remains
cumbersome and expensive. What is needed is an inexpensive method
of sequencing large numbers of RNA simultaneously in solution. The
method must be rapid and easy to perform. Methods of simultaneously
sequencing large numbers of RNA molecules would provide chemical
screens of cell cultures to identify drugs of interest, tissue,
blood and other biological sample bank screening. These methods
further would allow screening of RNA from tissue in
paraffin-blocks. These methods would also provide antibiotic
screening to determine drug resistance in microorganisms. This
disclosure meets that need.
SUMMARY OF THE DISCLOSURE
A universal method is disclosed for the sequencing preparation of
all classes of RNA. The method allows for sequencing for dozens to
more than thousands of samples simultaneously. Thus, disclosed is a
method for parallel sequencing target RNA from samples from
multiple sources while maintaining source identification. The
disclosed method includes providing samples of RNA comprising
target RNA from two or more sources and labeling, at the 3' end,
the RNA from the two or more sources with a first nucleic acid
adaptor that includes a nucleic acid sequence that differentiates
between the RNA from the two or more sources. The 3' end labeled
RNA is reverse transcribed to create a single stranded DNA
comprising the nucleic acid sequence that differentiates between
the RNA from the two or more sources. The resultant DNA is
amplified to create DNA amplification products that comprise the
nucleic acid sequence that differentiates between the RNA from the
two or more sources. Finally sequencing the DNA amplification
products identifies, in parallel, target RNA from samples from
multiple sources while maintaining source identification. In some
embodiments of the disclosed method, the 3' labeled RNA is pooled.
Also disclosed are kits for carrying out the disclosed method.
The advantages of the disclosed method over current protocols
includes, but is not limited to, a strand-specific sequencing of
all classes of RNA from any species including eukaryotes and
prokaryotes including total RNA, antibody-selected RNA, 5'DGE and
3'DGE selected fragments, polyA-selected RNA, cross-linked RNA
fragments from human, bacteria, and fungi. The disclosed method
also allows for sequencing of dozens to several thousands of
independent RNA samples simultaneously. The disclosed inventions
are very low cost and low time per sample compared to commercial
kits. The full protocol can take as little as approximately 6
hours.
The foregoing and other features of this disclosure will become
more apparent from the following detailed description of several
embodiments, which proceeds with reference to the accompanying
figures.
BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 is a schematic of an exemplary method of RNA sequencing as
disclosed herein.
FIG. 2 is a schematic of 3' ligation of a sequence tag (barcode) to
an RNA.
FIG. 3 is a schematic of the pooling of differently tagged
(barcoded) RNA for subsequent processing
FIG. 4 is a schematic first strand ssDNA synthesis.
FIG. 5 is a schematic a second adapter ligation (ssDNA/ssDNA) by 3'
linker ligation.
FIG. 6 is a schematic showing amplification of ssDNA encoding
information about the origin of the target RNA.
BRIEF DESCRIPTION OF SEQUENCES
The nucleic and amino acid sequences are shown using standard
letter abbreviations for nucleotide bases, and three letter code
for amino acids, as defined in 37 C.F.R. 1.822. If only one strand
of each nucleic acid sequence is shown, the complementary strand is
understood as included by any reference to the displayed strand.
All sequence database accession numbers referenced herein are
understood to refer to the version of the sequence identified by
that accession number as it was available on the designated
date.
DETAILED DESCRIPTION OF SEVERAL EMBODIMENTS
I. Summary of Terms
Unless otherwise noted, technical terms are used according to
conventional usage. Definitions of common terms in molecular
biology may be found in Benjamin Lewin, Genes IX, published by
Jones and Bartlet, 2008 (ISBN 0763752223); Kendrew et al. (eds.),
The Encyclopedia of Molecular Biology, published by Blackwell
Science Ltd., 1994 (ISBN 0632021829); and Robert A. Meyers (ed.),
Molecular Biology and Biotechnology: a Comprehensive Desk
Reference, published by VCH Publishers, Inc., 1995 (ISBN
9780471185710).
The singular terms "a," "an," and "the" include plural referents
unless context clearly indicates otherwise. Similarly, the word
"or" is intended to include "and" unless the context clearly
indicates otherwise. The term "comprises" means "includes." In case
of conflict, the present specification, including explanations of
terms, will control.
To facilitate review of the various embodiments of this disclosure,
the following explanations of specific terms are provided:
Amplification: To increase the number of copies of a nucleic acid
molecule, such as a DNA according the disclosed methods. The
resulting amplification products are called "amplicons."
Amplification of a nucleic acid molecule refers to use of a
technique that increases the number of copies of a nucleic acid
molecule (including fragments).
An example of amplification is the polymerase chain reaction (PCR),
in which a sample is contacted with a pair of oligonucleotide
primers under conditions that allow for the hybridization of the
primers to a nucleic acid template in the sample. The primers are
extended under suitable conditions, dissociated from the template,
re-annealed, extended, and dissociated to amplify the number of
copies of the nucleic acid. This cycle can be repeated. The product
of amplification can be characterized by such techniques as
electrophoresis, restriction endonuclease cleavage patterns,
oligonucleotide hybridization or ligation, and/or nucleic acid
sequencing.
Other examples of in vitro amplification techniques include
quantitative real-time PCR; reverse transcriptase PCR (RT-PCR);
real-time PCR (rt PCR); real-time reverse transcriptase PCR (rt
RT-PCR); nested PCR; strand displacement amplification (see U.S.
Pat. No. 5,744,311); transcription-free isothermal amplification
(see U.S. Pat. No. 6,033,881, repair chain reaction amplification
(see WO 90/01069); ligase chain reaction amplification (see
European patent publication EP-A-320 308); gap filling ligase chain
reaction amplification (see U.S. Pat. No. 5,427,930); coupled
ligase detection and PCR (see U.S. Pat. No. 6,027,889); and
NASBA.TM. RNA transcription-free amplification (see U.S. Pat. No.
6,025,134) amongst others.
Binding or stable binding (of an oligonucleotide): An
oligonucleotide, such as a probe or primer binds or stably binds to
a target nucleic acid, such as a nucleic acid with a PCR primer
tag, if a sufficient amount of the oligonucleotide forms base pairs
or is hybridized to its target nucleic acid. Binding can be
detected by either physical or functional properties.
Binding site: A region on a protein, DNA, or RNA to which other
molecules stably bind.
Capture moieties: Molecules or other substances that when attached
to a nucleic acid molecule, such as a DNA molecule, allow for the
capture of the nucleic acid molecule through interactions of the
capture moiety and something that the capture moiety binds to, such
as a particular surface and/or molecule, such as a specific binding
molecule that is capable of specifically binding to the capture
moiety. In some examples, a capture moiety is a biotin, which can
be captured by avidin and or streptavidin. In some embodiments, the
capture moiety, such as biotin, is attached to nucleic acid
sequence that is used to remove non-target RNA from a sample, such
as rRNA.
Contacting: Placement in direct physical association, including
both in solid or liquid form.
Control: A reference standard. A control can be a known value or
range of values indicative of basal levels or amounts or present in
a tissue or a cell or populations thereof. A control can also be a
cellular or tissue control, for example a tissue from a
non-diseased state and/or exposed to different environmental
conditions. A difference between a test sample and a control can be
an increase or conversely a decrease. The difference can be a
qualitative difference or a quantitative difference, for example a
statistically significant difference.
Covalently linked: Refers to a covalent linkage between atoms by
the formation of a covalent bond characterized by the sharing of
pairs of electrons between atoms. In one example, a covalent link
is a bond between an oxygen atom and a phosphorous atom, such as
phosphodiester bonds in the backbone of a nucleic acid strand.
Complementary: A double-stranded DNA or RNA strand consists of two
complementary strands of base pairs. Complementary binding occurs
when the base of one nucleic acid molecule forms a hydrogen bond to
the base of another nucleic acid molecule. Normally, the base
adenine (A) is complementary to thymidine (T) and uracil (U), while
cytosine (C) is complementary to guanine (G). For example, the
sequence 5'-ATCG-3' of one ssDNA molecule can bond to 3'-TAGC-5' of
another ssDNA to form a dsDNA. In this example, the sequence
5'-ATCG-3' is the reverse complement of 3'-TAGC-5'.
Nucleic acid molecules can be complementary to each other even
without complete hydrogen-bonding of all bases of each molecule.
For example, hybridization with a complementary nucleic acid
sequence can occur under conditions of differing stringency in
which a complement will bind at some but not all nucleotide
positions.
Detect: To determine if an agent (such as a signal or particular
nucleic acid, such as a RNA) is present or absent. In some
examples, this can further include quantification in a sample, or a
fraction of a sample, such as a particular cell or cells within a
tissue.
Detectable label: A compound or composition that is conjugated
directly or indirectly to another molecule to facilitate detection
of that molecule. Specific, non-limiting examples of labels include
fluorescent tags, enzymatic linkages, and radioactive isotopes. In
some examples, a label is attached to an antibody or nucleic acid
to facilitate detection of the molecule the antibody or nucleic
acid specifically binds.
DNA sequencing: The process of determining the nucleotide order of
a given DNA molecule. Generally, the sequencing can be performed
using automated Sanger sequencing (AB13730.times.1 genome
analyzer), pyrosequencing on a solid support (454 sequencing,
Roche), sequencing-by-synthesis with reversible terminations
(ILLUMINA.RTM. Genome Analyzer), sequencing-by-ligation (ABI
SOLiD.RTM.) or sequencing-by-synthesis with virtual terminators
(HELISCOPE.RTM.).
In some embodiments, DNA sequencing is performed using a chain
termination method developed by Frederick Sanger, and thus termed
"Sanger based sequencing" or "SBS." This technique uses
sequence-specific termination of a DNA synthesis reaction using
modified nucleotide substrates. Extension is initiated at a
specific site on the template DNA by using a short oligonucleotide
primer complementary to the template at that region. The
oligonucleotide primer is extended using DNA polymerase in the
presence of the four deoxynucleotide bases (DNA building blocks),
along with a low concentration of a chain terminating nucleotide
(most commonly a di-deoxynucleotide). Limited incorporation of the
chain terminating nucleotide by the DNA polymerase results in a
series of related DNA fragments that are terminated only at
positions where that particular nucleotide is present. The
fragments are then size-separated by electrophoresis a
polyacrylamide gel, or in a narrow glass tube (capillary) filled
with a viscous polymer. An alternative to using a labeled primer is
to use labeled terminators instead; this method is commonly called
"dye terminator sequencing."
"Pyrosequencing" is an array-based method, which has been
commercialized by 454 Life Sciences. In some embodiments of the
array-based methods, single-stranded DNA is annealed to beads and
amplified via EmPCR.RTM.. These DNA-bound beads are then placed
into wells on a fiber-optic chip along with enzymes that produce
light in the presence of ATP. When free nucleotides are washed over
this chip, light is produced as the PCR amplification occurs and
ATP is generated when nucleotides join with their complementary
base pairs. Addition of one (or more) nucleotide(s) results in a
reaction that generates a light signal that is recorded, such as by
the charge coupled device (CCD) camera, within the instrument. The
signal strength is proportional to the number of nucleotides, for
example, homopolymer stretches, incorporated in a single nucleotide
flow.
High throughput technique: Through a combination of robotics, data
processing and control software, liquid handling devices, and
detectors, high throughput techniques allows the rapid screening of
potential reagents, conditions, or targets in a short period of
time, for example in less than 24, less than 12, less than 6 hours,
or even less than 1 hour.
Hybridization: Oligonucleotides and their analogs hybridize by
hydrogen bonding, which includes Watson-Crick, Hoogsteen or
reversed Hoogsteen hydrogen bonding, between complementary bases.
Generally, nucleic acid consists of nitrogenous bases that are
either pyrimidines (cytosine (C), uracil (U), and thymine (T)) or
purines (adenine (A) and guanine (G)). These nitrogenous bases form
hydrogen bonds between a pyrimidine and a purine, and the bonding
of the pyrimidine to the purine is referred to as "base pairing."
More specifically, A will hydrogen bond to T or U, and G will bond
to C. "Complementary" refers to the base pairing that occurs
between two distinct nucleic acid sequences or two distinct regions
of the same nucleic acid sequence.
"Specifically hybridizable" and "specifically complementary" are
terms that indicate a sufficient degree of complementarity such
that stable and specific binding occurs between the oligonucleotide
(or its analog) and the DNA, RNA, and or DNA-RNA hybrid target. The
oligonucleotide or oligonucleotide analog need not be 100%
complementary to its target sequence to be specifically
hybridizable. An oligonucleotide or analog is specifically
hybridizable when there is a sufficient degree of complementarity
to avoid non-specific binding of the oligonucleotide or analog to
non-target sequences under conditions where specific binding is
desired. Such binding is referred to as specific hybridization.
Isolated: An "isolated" biological component (such as a protein, a
nucleic RNA, for example target RNA) has been substantially
separated or purified away from other biological components in the
cell of the organism in which the component naturally occurs, for
example, extra-chromatin DNA and RNA, proteins and organelles.
Nucleic acids and proteins that have been "isolated" include
nucleic acids and proteins purified by standard purification
methods. The term also embraces nucleic acids and proteins prepared
by recombinant expression in a host cell as well as chemically
synthesized nucleic acids. It is understood that the term
"isolated" does not imply that the biological component is free of
trace contamination, and can include nucleic acid molecules that
are at least 50% isolated, such as at least 75%, 80%, 90%, 95%,
98%, 99%, or even 100% isolated.
Nucleic acid (molecule or sequence): A deoxyribonucleotide,
ribonucleotide or deoxyribonucleotide-ribonucleotide polymer
including without limitation, cDNA, mRNA, genomic DNA, and
synthetic (such as chemically synthesized) DNA or RNA or hybrids
thereof. The nucleic acid can be double-stranded (ds) or
single-stranded (ss). Where single-stranded, the nucleic acid can
be the sense strand or the antisense strand. Nucleic acids can
include natural nucleotides (such as A, T/U, C, and G), and can
also include analogs of natural nucleotides, such as labeled
nucleotides.
The major nucleotides of DNA are deoxyadenosine 5'-triphosphate
(dATP or A), deoxyguanosine 5'-triphosphate (dGTP or G),
deoxycytidine 5'-triphosphate (dCTP or C) and deoxythymidine
5'-triphosphate (dTTP or T). The major nucleotides of RNA are
adenosine 5'-triphosphate (ATP or A), guanosine 5'-triphosphate
(GTP or G), cytidine 5'-triphosphate (CTP or C) and uridine
5'-triphosphate (UTP or U). Nucleotides include those nucleotides
containing modified bases, modified sugar moieties, and modified
phosphate backbones, for example as described in U.S. Pat. No.
5,866,336 to Nazarenko et al.
Examples of modified base moieties which can be used to modify
nucleotides at any position on its structure include, but are not
limited to: 5-fluorouracil, 5-bromouracil, 5-chlorouracil,
5-iodouracil, hypoxanthine, xanthine, acetylcytosine,
5-(carboxyhydroxylmethyl) uracil,
5-carboxymethylaminomethyl-2-thiouridine,
5-carboxymethylaminomethyluracil, dihydrouracil,
beta-D-galactosylqueosine, inosine, N-6-sopentenyladenine,
1-methylguanine, 1-methylinosine, 2,2-dimethylguanine,
2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methyl
cytosine, N6-adenine, 7-methylguanine, 5-methylaminomethyluracil,
methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine,
5'-methoxycarboxymethyluracil, 5-methoxyuracil,
2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid,
pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil,
2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5-oxyacetic acid
methylester, uracil-S-oxyacetic acid, 5-methyl-2-thiouracil,
3-(3-amino-3-N-2-carboxypropyl) uracil, 2,6-diaminopurine and
biotinylated analogs, amongst others.
Examples of modified sugar moieties which may be used to modify
nucleotides at any position on its structure include, but are not
limited to arabinose, 2-fluoroarabinose, xylose, and hexose, or a
modified component of the phosphate backbone, such as
phosphorothioate, a phosphorodithioate, a phosphoramidothioate, a
phosphoramidate, a phosphordiamidate, a methylphosphonate, an alkyl
phosphotriester, or a formacetal or analog thereof.
Primers: Short nucleic acid molecules, such as a DNA
oligonucleotide, which can be annealed to a complementary target
nucleic acid molecule by nucleic acid hybridization to form a
hybrid between the primer and the target nucleic acid strand. A
primer can be extended along the target nucleic acid molecule by a
polymerase enzyme. Therefore, primers can be used to amplify a
target nucleic acid molecule, wherein the sequence of the primer is
specific for the target nucleic acid molecule, for example so that
the primer will hybridize to the target nucleic acid molecule under
very high stringency hybridization conditions.
The specificity of a primer increases with its length. Thus, for
example, a primer that includes 30 consecutive nucleotides will
anneal to a target sequence with a higher specificity than a
corresponding primer of only 15 nucleotides. Thus, to obtain
greater specificity, probes and primers can be selected that
include at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50 or more
consecutive nucleotides.
In particular examples, a primer is at least 15 nucleotides in
length, such as at least 5 contiguous nucleotides complementary to
a target nucleic acid molecule. Particular lengths of primers that
can be used to practice the methods of the present disclosure
include primers having at least 5, at least 10, at least 15, at
least 16, at least 17, at least 18, at least 19, at least 20, at
least 21, at least 22, at least 23, at least 24, at least 25, at
least 26, at least 27, at least 28, at least 29, at least 30, at
least 31, at least 32, at least 33, at least 34, at least 35, at
least 36, at least 37, at least 38, at least 39, at least 40, at
least 45, at least 50, or more contiguous nucleotides complementary
to the target nucleic acid molecule to be amplified, such as a
primer of 5-60 nucleotides, 15-50 nucleotides, 15-30 nucleotides or
greater.
Primer pairs can be used for amplification of a nucleic acid
sequence, for example, by PCR, or other nucleic-acid amplification
methods known in the art. An "upstream" or "forward" primer is a
primer 5' to a reference point on a nucleic acid sequence. A
"downstream" or "reverse" primer is a primer 3' to a reference
point on a nucleic acid sequence. In general, at least one forward
and one reverse primer are included in an amplification reaction.
PCR primer pairs can be derived from a known sequence, for example,
by using computer programs intended for that purpose such as Primer
(Version 0.5, .COPYRGT. 1991, Whitehead Institute for Biomedical
Research, Cambridge, Mass.).
Methods for preparing and using primers are described in, for
example, Sambrook et al. (1989) Molecular Cloning: A Laboratory
Manual, Cold Spring Harbor, N.Y.; Ausubel et al. (1987) Current
Protocols in Molecular Biology, Greene Publ. Assoc. &
Wiley-Intersciences.
Probe: A probe comprises an isolated nucleic acid capable of
hybridizing to a target nucleic acid. A detectable label or
reporter molecule can be attached to a probe. Typical labels
include radioactive isotopes, enzyme substrates, co-factors,
ligands, chemiluminescent or fluorescent agents, haptens, and
enzymes.
Methods for labeling and guidance in the choice of labels
appropriate for various purposes are discussed, for example, in
Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold
Spring Harbor Laboratory Press (1989) and Ausubel et al., Current
Protocols in Molecular Biology, Greene Publishing Associates and
Wiley-Intersciences (1987).
Probes are generally at least 5 nucleotides in length, such as at
least 10, at least 20, at least 21, at least 22, at least 23, at
least 24, at least 25, at least 26, at least 27, at least 28, at
least 29, at least 30, at least 31, at least 32, at least 33, at
least 34, at least 35, at least 36, at least 37, at least 38, at
least 39, at least 40, at least 41, at least 42, at least 43, at
least 44, at least 45, at least 46, at least 47, at least 48, at
least 49, at least 50 at least 51, at least 52, at least 53, at
least 54, at least 55, at least 56, at least 57, at least 58, at
least 59, at least 60, or more contiguous nucleotides complementary
to the target nucleic acid molecule, such as 50-60 nucleotides,
20-50 nucleotides, 20-40 nucleotides, 20-30 nucleotides or
greater.
Polymerizing agent: A compound capable of reacting monomer
molecules (such as nucleotides) together in a chemical reaction to
form linear chains or a three-dimensional network of polymer
chains. A particular example of a polymerizing agent is polymerase,
an enzyme which catalyzes the 5' to 3' elongation of a primer
strand complementary to a nucleic acid template. Examples of
polymerases that can be used to amplify a nucleic acid molecule
include, but are not limited to the E. coli DNA polymerase I,
specifically the Klenow fragment which has 3' to 5' exonuclease
activity, Taq polymerase, reverse transcriptase (such as HIV-1 RT),
E. coli RNA polymerase, and wheat germ RNA polymerase II.
The choice of polymerase is dependent on the nucleic acid to be
amplified. If the template is a single-stranded DNA molecule, a
DNA-directed DNA or RNA polymerase can be used; if the template is
a single-stranded RNA molecule, then a reverse transcriptase (such
as an RNA-directed DNA polymerase) can be used.
Sample: A sample, such as a biological sample, that includes
biological materials (such as nucleic acid and proteins, for
example RNA) obtained from an organism or a part thereof, such as a
plant, animal, bacteria, and the like. In particular embodiments,
the biological sample is obtained from an animal subject, such as a
human subject. A biological sample is any solid or fluid sample
obtained from, excreted by or secreted by any living organism,
including without limitation, single celled organisms, such as
bacteria, yeast, protozoans, and amebas among others, multicellular
organisms (such as plants or animals, including samples from a
healthy or apparently healthy human subject or a human patient
affected by a condition or disease to be diagnosed or investigated,
such as cancer). For example, a biological sample can be a
biological fluid obtained from, for example, blood, plasma, serum,
urine, bile, ascites, saliva, cerebrospinal fluid, aqueous or
vitreous humor, or any bodily secretion, a transudate, an exudate
(for example, fluid obtained from an abscess or any other site of
infection or inflammation), or fluid obtained from a joint (for
example, a normal joint or a joint affected by disease, such as a
rheumatoid arthritis, osteoarthritis, gout or septic arthritis). A
sample can also be a sample obtained from any organ or tissue
(including a biopsy or autopsy specimen, such as a tumor biopsy) or
can include a cell (whether a primary cell or cultured cell) or
medium conditioned by any cell, tissue or organ.
Specific Binding Agent: An agent that binds substantially or
preferentially only to a defined target such as a protein, enzyme,
polysaccharide, oligonucleotide, DNA, RNA, or a small molecule. In
an example, a "capture moiety specific binding agent" is capable of
binding to a capture moiety that is covalently linked to a DNA
molecule.
A nucleic acid-specific binding agent binds substantially only to
the defined nucleic acid, such as RNA, DNA or a RNA-DNA hybrid, or
to a specific region within the nucleic acid.
Tissue: A plurality of functionally related cells. A tissue can be
a suspension, a semi-solid, or solid. Tissue includes cells
collected from a subject such as blood, cervix, uterus, lymph
nodes, breast, skin, and other organs.
Under conditions that permit binding: A phrase used to describe any
environment that permits the desired activity, for example
conditions under which two or more molecules, such as nucleic acid
molecules and/or protein molecules, can bind.
Suitable methods and materials for the practice or testing of this
disclosure are described below. Such methods and materials are
illustrative only and are not intended to be limiting. Other
methods and materials similar or equivalent to those described
herein can be used. For example, conventional methods well known in
the art to which this disclosure pertains are described in various
general and more specific references, including, for example,
Sambrook et al., Molecular Cloning: A Laboratory Manual, 2d ed.,
Cold Spring Harbor Laboratory Press, 1989; Sambrook et al.,
Molecular Cloning: A Laboratory Manual, 3d ed., Cold Spring Harbor
Press, 2001; Ausubel et al., Current Protocols in Molecular
Biology, Greene Publishing Associates, 1992 (and Supplements to
2000); Ausubel et al., Short Protocols in Molecular Biology: A
Compendium of Methods from Current Protocols in Molecular Biology,
4th ed., Wiley & Sons, 1999; Harlow and Lane, Antibodies: A
Laboratory Manual, Cold Spring Harbor Laboratory Press, 1990; and
Harlow and Lane, Using Antibodies: A Laboratory Manual, Cold Spring
Harbor Laboratory Press, 1999. In addition, the materials, methods,
and examples are illustrative only and not intended to be
limiting.
II. Overview
Disclosed herein is a novel method of identifying the sequence of a
set of RNAs in a multiplex setting. FIG. 1 depicts a non-limiting
example of the disclosed methods. As shown in FIG. 1, in the first
step of the disclosed method, RNA is labeled (or barcoded) by
attachment, such as ligation, of a 3' adaptor, which is typically
coded to the source of the RNA, for example the specific sample.
Optionally, one can perform oligo-based RNA depletion, such as
depletion of rRNA, to remove RNA, which may interfere with the
method or analysis. Once barcoded, individual samples of RNA can be
pooled. The number of samples that can be pooled is only limited by
the complexity of the barcodes, which is dictated by length, for
example as the length of the barcode is increased by one
nucleotide, the complexity of the barcode, or number of barcodes
available is increased by 4. In the next step of the method,
reverse transcription/first strand cDNA synthesis is performed with
an adaptor-specific primer that specifically binds the 3' adaptor
that has been attached to the RNA. During the reverse
transcription/first strand cDNA synthesis information about the
sequence of the RNA and the barcode is imprinted in the resulting
ssDNA, thus locking in this information. The next step in the
method is preparation of cDNA for enrichment. There are several
ways that this can be accomplished. In one example, a second
adapter ligation (ssDNA/ssDNA) by 3' linker ligation is performed.
The adapter can be universal or can be barcoded, for example to
increase the depth of multiplexing. In another example, 2.sup.nd
strand synthesis can be performed, for example to make a double
stranded cDNA (ds cDNA). The now ds cDNA can then be end repaired,
and in some examples dsDNA adapter ligated. In another example, the
cDNA can be treated with a terminal transferase followed by
isothermal amplification. The resulting DNA can be amplified, for
example by PCR prior to sequence analysis. This enrichment
effectively increases the signal of the sequencing.
With reference to FIG. 2, as discussed above, in the first step of
the disclosed method, there is a first ligation with a 3' adapter
to label the RNA with a sequence label (barcode) that can be
indexed to the origin or source of the sample. The adaptor can be
RNA or DNA with preferably a 2 to 10 nucleotide barcode on the
adaptor (or longer) with any modification (e.g., adenylation) which
is compatible with a ligation reaction. In some embodiments,
different adaptors with different barcodes are added to a single
sample, such as a single well. For example, instead of adding a
single unique barcode per sample, about 2 to about 10, such as 2,
3, 4 5, 6, 7, 8, 9, 10 or more, different adapters each containing
a unique barcode sequence are added to each sample. It has been
found that adding set of barcodes, such as between about 2-4
different adapters, each containing unique barcode sequence,
increases ligation efficiency and experimental uniformity. In each
set, each barcode is unique, and in all sets all barcode sequences
are unique between each other.
By way of example, if one considers samples in a 96 well plate
(other larger or smaller formats are contemplated as well), one
sample in one well would have 1 barcode (or a set of a
few-to-several unique barcodes) and a second sample in a well would
have a second barcode (or a second set of a few-to-several
different unique barcodes) and so on, such that 96 samples would
have 96 different barcodes (or 96 different unique barcodes sets)
and 573 samples would have 573 different barcodes and the like. The
sequences of the barcodes (which could be referred to as indexing
sequences) are designed so that there is no self-ligation or cross
ligation among the barcode sequences. FIG. 3 represents 96 ligated
and barcoded different RNAs. The barcoded RNAs can then be pooled,
as the information about the origin or source of the RNA in the
sample is now set.
With reference to FIG. 4, in the next step, a reverse transcript of
the RNA is generated using a primer specific to the adapter and a
review transcriptase, such as a RNAseH-minus reverse transcriptase.
This generates a ssDNA that encodes the RNA as well as the
information about origin or source, in the form of the barcode. The
primer and the RNA can be removed, such that they do not interfere
with subsequent steps of the method and/or analysis. For example,
the RT primer can be digested using ExoSAP, Exo I or any other
ssDNA specific nuclease. The RNA can be degraded from the RNA/cDNA
hybrid using NaOH, RNAseH or any other enzymatic or chemical
method. In some examples, the resulting solution is cleaned up
using Silane beads with low ethanol concentrations to remove the
majority of leftover primers.
The next step in the method is preparation of ssDNA for enrichment.
With reference to FIG. 5, in some embodiments of the disclosed
method, a second adapter ligation (ssDNA/ssDNA) by 3' linker
ligation is performed. The adapter can be universal or can be
barcoded. The resultant nucleic acids can then be sequenced using
any method of DNA sequencing available.
With reference to FIG. 6, PCR enrichment of the RNA-seq library is
performed. Any standard PCR polymerase can be used. For example
Phusion.RTM. polymerase can be used under standard conditions. In
some examples, the resultant PCR products are purified to remove
primers, primer-dimers, short fragments, PCR polymerase, and
nucleotides.
The 3' labeled RNA can optionally be pooled. The 3' end of single
stranded DNA can be labeled with a second nucleic acid adaptor that
comprises a site for binding of a PCR primer. The second nucleic
acid adaptor can be a sequencing adaptor. In addition, the second
nucleic acid adaptor can differentiate between single stranded DNA
from two or more sources. Optionally, the sample can be depleted of
non-target RNA by using one or more probes that specifically
hybridize to the non-target RNA and wherein one or more probes
comprise a label that facilitates the removal of the probe from the
sample. The label includes, but is not limited to, biotin. It is to
be understood that the first or second nucleic acid adaptor can be
blocked at the 3'end. The first or second nucleic acid adaptor can
be RNA, DNA or a RNA-DNA hybrid. The nucleic acid sequence that
differentiates between the RNA or single stranded DNA from the two
or more sources is preferably at least two nucleotides in length.
Optionally, the reverse transcription primers are removed or
degraded. The samples of different origins can be samples of the
same cell type and/or tissue type that have been exposed to
different environmental conditions, said conditions including, but
not limited to, contacts with different test agents. The target RNA
can be mRNA and the differences in expression of the mRNA are
measured across samples from different sources. The disclosed
invention further comprises quantifying the sequenced target RNAs
of samples from multiple sources. The sequenced target RNAs can be
sorted to their respective sources.
The benefits of the disclosed method include reduced costs. In
addition, the disclosed method is a very efficient method for
sequencing RNA biopsy material in paraffin-embedded blocks. The
disclosed method is particularly useful for crosslinked RNA samples
from cells and tissues. The disclosed method has been used in
testing hundreds of poly-A selected samples, 5'-DGE, and 3'-DGE RNA
samples. The disclosed method has been used in low complexity
samples such as yeast or bacterial genomes where a small number of
reads with deep multiplexing is required. The disclosed method
allows for sequencing of dozens to thousands of RNA samples
simultaneously.
III. Description of Several Embodiments
Disclosed is a method for parallel sequencing target RNA from
samples (such as multiple target RNAs from multiple, for example
one or more, samples) from multiple sources while maintaining
source identification. The disclosed methods use a unique coding
system to maintain the information about where a sample came from,
so that a user, for example a laboratory worker, can keep track of
the origin of a sample based on sequence information, such as that
contained in a sequencing read of a nucleic acid sequencing system.
The disclosed method includes providing samples of RNA, such as one
or more, for example two or more samples of RNA, comprising target
RNA from two or more sources. It is contemplated that the sources
can be the same source, for example the same organism, at the same
or different time points, for example when some one is looking at
differences in RNA expression as a function of time or tissue,
amongst others. In the disclosed method, the RNA is labeled at the
3' end (such as through a ligation reaction) with a first nucleic
acid adaptor that comprises a nucleic acid sequence that
differentiates between the RNA from the two or more sources. In
other words, the RNA is tagged with a unique sequence identifier on
the 3' end that distinguishes the RNA from one origin from an RNA
of another origin, which in some examples can further include a
site for binding of a PCR primer and/or a sequencing adaptor. The
adaptor can be RNA and/or DNA and is about 2 to about 10
nucleotides is length, although longer are contemplated, for
example the adaptor is about 2 to about 10 nucleotides in length,
such as about 2, about 3, about 4, about 5, about 6, about 7, about
8, about 9, or about 10 nucleotides in length, such as about 2 to
about 8, about 3 to about 10, about 5 to about 8 and the like. In
some embodiments, the RNA is also labeled at the 5' end (such as
through a ligation reaction) with a first 5' nucleic acid adaptor
that comprises a nucleic acid sequence that differentiates between
the RNA from the two or more sources, which in some examples can
further include a site for binding of a PCR primer and/or a
sequencing adaptor. The addition at the 5'-end of RNA can occur
before or after the addition at the 3'-end. The labeled RNA (5'
and/or 3') is reverse transcribed to create a single stranded DNA
comprising the nucleic acid sequence that differentiates between
the RNA from the two or more sources. In some examples the RNA is
treated to block addition to the 3' end during the 5' ligation. In
some embodiments, the single stranded RNA (such as the target RNA)
can be labeled at the 3' end with a second nucleic acid adaptor
that comprises a site for binding of a PCR primer. In some
embodiments, the single stranded RNA (such as the target RNA) can
be labeled at the 5' end with a second nucleic acid adaptor that
comprises a site for binding of a PCR primer.
The single stranded DNA is amplified to create DNA amplification
products that comprise the nucleic acid sequence that
differentiates between the RNA from the two or more sources and the
DNA amplification products are sequenced, thereby parallel
sequencing target RNA from samples from multiple sources while
maintaining source identification.
In some embodiments, the 3' labeled RNAs are pooled. For example,
once the information about the origin of the RNA is locked in by
the addition of the 3' label, the samples can be pooled and treated
essentially identically for the remainder of whatever test, trial,
or experiment is being conducted, as the information about the
origin of the RNA can always be determined by the sequence. This
gives the disclosed techniques the power to be used in multiplexing
reactions, where one would want all the samples to be treated
identically, which can be very important for experiments that rely
on the analysis of the relative or absolute levels of RNA amongst
multiple sources.
In some embodiments, the single stranded DNA can be labeled at the
3' end with a second nucleic acid adaptor that comprises a site for
binding of a PCR primer. In some embodiments, the single stranded
DNA can be labeled at the 5' end with a second nucleic acid adaptor
that comprises a site for binding of a PCR primer. In some examples
the second nucleic acid comprises a sequencing adaptor. In some
embodiments, the second nucleic acid adaptor comprises a second
nucleic acid sequence that can differentiate between single
stranded DNA from two or more sources. In this way, the information
about the origin can be further multiplexed. By way of example,
this can be used to create a nested hierarchy about the origin of
the RNA, for example, hierarchy by organism, tissue type, time
point and so on, which allows all of the individual samples to be
pooled and analyzed simultaneously. In some examples, the second
nucleic acid adaptor comprises a site for binding of a PCR primer.
In some embodiments, the single stranded DNA is pooled with single
stranded DNA from one or more additional sources, wherein the
single stranded DNA from one or more additional sources is
similarly labeled.
In some embodiments, the samples are depleted of non-target RNA. By
way of example, in a cellular system, much of the RNA in a sample,
such as in a lysed sample is comprised of rRNA, which may not be of
interest for analysis, and may complicate the analysis. Thus, it
can be useful to deplete a sample of non-target RNA. It is to be
understood that rRNA depletion is very important for quality of
sequencing data, because rRNAs and regulatory RNAs are responsible
for 95% to 98% of sequencing reads. Any RNA that does not need to
be sequenced can be depleted, including ribosomal RNAs, tRNAs,
regulatory RNAs and introns. The rRNA depletion works by
hybridizing RNA samples to probes antisense to the RNA to be
depleted, where the antisense probes include a capture moiety that
can be captured by a specific binding agent. In some examples,
depleting the samples of non-target RNA comprises using one or more
probes that specifically hybridize to the non-target RNA, wherein
the one or more probes comprise a label that facilitates removal of
the probe from the sample. In some examples the one or more probes
is a plurality of probes, wherein probes in the plurality are
selected to tile across the sequence of the non-target RNA. In some
examples, the label comprises biotin. In some examples, the probes
are biotinylated antisense probes that deplete ribosomal RNAs (18
S, 28 S 5.8 S and 5 S) and regulatory RNAs, like snRNAs. The
probe-RNA is later bound to streptavidin beads to physically remove
the target RNAs from the solution. Due to the GC-rich sequence of
28 S, it is better to use not only biotinylated UTP, but also
biotinylated CTP.
In some embodiments, the reverse transcription primers are removed
and/or degraded. In some embodiments, the RNA is removed and/or
degraded after first strand synthesis of ssDNA. In some examples,
samples are cleaned using Silane beads to remove adaptors that did
not ligate. The RNA samples can be pooled in one of several pools
during the clean up step. Pools can later be coded separately,
allowing even deeper multiplexing. The cleaning of samples can be
performed using Silane beads or other beads such as solid phase
reversible immobilization (SPRI) beads. Using beads for the clean
up allows for use of robotics for the entire process thereby
reducing labor cost.
In some examples, the samples of different origins comprise samples
of the same cell type and/or tissue type exposed to different
environmental conditions. In some examples the different
environmental conditions are contact with different test agents,
for example to look at the effect of such different conditions on
the content of the RNA in the samples.
In some embodiments, the target RNA is mRNA, and differences in
expression of the mRNA are measured across samples from different
sources. In some embodiments, the sequenced target RNAs of samples
from multiple sources are quantified. In some embodiments, the
sequenced target RNAs are sorted to their respective sources.
There are numerous applications for the disclosed methods. Any
application requiring high throughput sequencing of many eukaryotic
or prokaryotic RNAs is particularly suited for the disclosed
method. These include, but are not limited to, chemical screens of
cell cultures to determine drugs of interest. Another use for the
disclosed method is RNA/DNA targeting screens such as siRNA/shRNA.
The disclosed method can be used for tissue, blood and other
biological sample bank screening. In addition, the disclosed method
can be used for screening RNA from paraffin block cells or tissues.
The disclosed method can be used for microbiome screening. Also,
the disclosed method can be used for antibiotic screening of
microorganisms to determine antibiotic resistance. Expression
profile screening can be performed using the disclosed method.
Appropriate samples for use in the methods disclosed herein include
any conventional biological sample obtained from an organism or a
part thereof that includes RNA to be analyzed, such as a plant,
animal, bacteria, and the like. In particular embodiments, the
biological sample is obtained from an animal subject, such as a
human subject. A biological sample is any solid or fluid sample
obtained from, excreted by or secreted by any living organism,
including without limitation, single celled organisms, such as
bacteria, yeast, protozoans, and amebas among others, multicellular
organisms (such as plants or animals, including samples from a
healthy or apparently healthy human subject or a human patient
affected by a condition or disease to be diagnosed or investigated,
such as cancer). For example, a biological sample can be a
biological fluid obtained from, for example, blood, plasma, serum,
urine, bile, ascites, saliva, cerebrospinal fluid, aqueous or
vitreous humor, or any bodily secretion, a transudate, an exudate
(for example, fluid obtained from an abscess or any other site of
infection or inflammation), or fluid obtained from a joint (for
example, a normal joint or a joint affected by disease, such as a
rheumatoid arthritis, osteoarthritis, gout or septic arthritis). A
sample can also be obtained from any organ or tissue (including a
biopsy or autopsy specimen, such as a tumor biopsy) or can include
a cell (whether a primary cell or cultured cell) or medium
conditioned by any cell, tissue or organ. Exemplary samples
include, without limitation, cells, cell lysates, blood smears,
cytocentrifuge preparations, cytology smears, bodily fluids (e.g.,
blood, plasma, serum, saliva, sputum, urine, bronchoalveolar
lavage, semen, etc.), tissue biopsies (e.g., tumor biopsies),
fine-needle aspirates, and/or tissue sections (e.g., cryostat
tissue sections and/or paraffin-embedded tissue sections). In other
examples, the sample includes circulating tumor cells (which can be
identified by cell surface markers). In particular examples,
samples are used directly (e.g., fresh or frozen), or can be
manipulated prior to use, for example, by fixation (e.g., using
formalin) and/or embedding in wax (such as formalin-fixed
paraffin-embedded (FFPE) tissue samples). It will appreciated that
any method of obtaining tissue from a subject can be utilized, and
that the selection of the method used will depend upon various
factors such as the type of tissue, age of the subject, or
procedures available to the practitioner. Standard techniques for
acquisition of such samples are available. See, for example
Schluger et al., J. Exp. Med. 176:1327-33 (1992); Bigby et al., Am.
Rev. Respir. Dis. 133:515-18 (1986); Kovacs et al., NEJM 318:589-93
(1988); and Ognibene et al., Am. Rev. Respir. Dis. 129:929-32
(1984).
Kits
A kit is provided for parallel sequencing target RNA from samples
from multiple sources while maintaining source identification of
nucleic acid probes and other reagents disclosed herein for use in
the disclosed invention. In such a kit, an appropriate amount of
one or more of the nucleic acid adaptors is provided in one or more
containers or held on a substrate. A nucleic acid adaptor may be
provided suspended in an aqueous solution or as a freeze-dried or
lyophilized powder, for instance. The container(s) can be any
conventional container that is capable of holding the supplied
form, for instance, microfuge tubes, ampoules, or bottles. The kits
can include either labeled or unlabeled nucleic acid probes. The
amount of nucleic acid probe supplied in the kit can be any
appropriate amount, and may depend on the target market to which
the product is directed. The kit for parallel sequencing target RNA
from samples from multiple sources while maintaining source
identification comprises a first nucleic acid adaptor for labeling,
at the 3' end, the RNA from the two or more sources that comprises
a nucleic acid sequence that differentiates between the RNA from
the two or more sources and a second nucleic acid adaptor for end
labeling the 3' end of single stranded DNA, wherein the second
nucleic acid adaptor comprises a site for binding of a PCR
primer.
The following examples are provided to illustrate certain
particular features and/or embodiments. These examples should not
be construed to limit the invention to the particular features or
embodiments described.
EXAMPLES
Example 1
The following protocol is used as a non-limiting example of the
methods disclosed herein. While specific times and reagents are
specified, it is contemplated that different, albeit similar
reagents, times, and temperatures can be employed by those of
ordinary skill in the art with minimal experimentation, given the
guidance presented herein.
Multiplexing version: The first 9 nucleotides of the first read
will contain a barcode (reverse & complement), where the
9.sup.th nucleotide will always be the same for each barcode
(A/T).
Each sample in the single pool has the same molarity. A Bravo robot
or 96-well pipettor could be used for 48-96 samples.
Use selected RNA or upto 250 ng of total RNA/sample.
Fragment and dephosphorylate RNA samples with FastAP and PNK.
Step A. First Ligation (RNA/RNA or RNA/DNA) 3' Linker Ligation
Mix RNA+adapter+DMSO. Heat at 70.degree. C. for 2 min.fwdarw.put on
ice
Perform reaction as follows:
TABLE-US-00001 Ligation Mix 1 tube N tubes Dephosphorylated RNA, 5
ng 5.5 (6) .mu.l 70 C. Barcoded adapter/linker, 100 pmoles 1 .mu.l
2 min .fwdarw. ice DMSO (100%) 1 .mu.l Add master-mix 10.times. NEB
ligase 1 Buffer 2 .mu.l DMSO (100%) 0.8 .mu.l ATP (100 mM) (fresh
from -80.degree. C.) 0.2 .mu.l PEG 8000 (50%) 8 .mu.l RNase
inhibitor 0.3 .mu.l T4 RNA Ligase 1, HiConc, 36 Units 1.2 .mu.l
Total 20 .mu.l NOTE: use less barcoded adapter for small amounts of
RNA.
T4 RNA Ligase 1, HiConc-custom NEB order, 30 U/.mu.l
Mix well many times or pipette using low-retention tips. Incubate
at 23.degree. C. for 1 hour 30 minutes.
Step B. Silane barcoded adapter cleanup:
Take 15 .mu.l of Silane beads/sample, rinse with RLT buffer, and
remove all supernatant from the beads. Bind ligation reaction with
3.times. volume of freshly added RLT and 0.5.times. (RNA+RLT
volume) EtOH. Mix well. Wash beads in 123 .mu.l of 70% EtOH twice
off of magnet. Place on magnet and discard supernatant. Pool
samples during second 70% ethanol wash. You can pool 4-96 samples
per pool. Let air-dry at room temperature for 3-10 minutes Elute in
100-200 .mu.l H.sub.2O (no depletion protocol) or 25-90 .mu.l
H.sub.2O (rRNA depletion protocol) and re-concentrate your sample
with a Zymo column or Silane. Elute in 14 .mu.l H.sub.2O (no
depletion protocol, go to RT directly). Continue to Step C. NOTE:
For a large number of samples, the Zymo RNA concentrator kit can be
used for the entire cleanup instead of Silane beads, which will
reduce time and cost.
Step C (Optional). Perform oligo-based rRNA depletion after
RNA-adapter ligation when needed. Use 10.times.rRNA probes mix
(18s+28s+5.8s+5s+other regulatory RNAs) with your sample (500 ng of
rRNA probe mix for 50 ng of input). Hybridize in large tubes. Heat
Denature RNA+probes at 72.degree. C. for 2 minutes. Make a 50 .mu.l
reaction mix, consisting of:
TABLE-US-00002 RNA oligos mix (500 ng) 2 .mu.l 2.times. Hyb Buffer
(heated to 72 C.) 25 .mu.l Ligated RNA + Adapter (100 ng) 23 .mu.l
Total (scale up if needed) 50 .mu.l
Bind at 70.degree. C. for 40 min in ThermoMixer with shaking
Prepare Streptavidin Beads after 30 minutes of incubation. Mix
beads well, take 12 .mu.l of Streptavidin beads per pool (around 40
.mu.U4 .mu.g of used rRNA probes.). Place beads on magnet, remove
supernatant. Wash the beads in 50 .mu.l of Hybridization Buffer.
Wash beads in 100 .mu.l of solution A for 2 min. Wash beads in 100
.mu.l of solution B. Wash beads in 100 .mu.l of 1.times.
Hybridization Buffer. Repeat a few times. Resuspend beads in 10
.mu.l of 1.times. Hybridization Buffer using in shaking ThermoMixer
(70.degree. C.).
Probe removal (Binding rRNA hybrids to beads): Add pre-warmed
streptavidin beads to hybridization reaction. Incubate at
68.degree. C. for 15 min on ThermoMixer. Quickly place on the
magnet; quickly transfer ALL Supernatant (which contains rRNA
depleted sample) to fresh tube.
Silane sample cleanup of rRNA depleted sample: Take 20 .mu.l of
Silane beads/sample, add some RLT, remove all supernatant from the
beads. Bind with 3.times. volume of freshly added RLT and
1.times.(RNA+RLT volume) EtOH, mix well. Wash beads in 123 ul of
70% EtOH twice off the magnet, Place on magnet and discard
supernatant. Let air-dry at RT for 3-10 minutes. Elute 14 .mu.l
H.sub.2O
Estimate that the RT primer will be in at least 5.times. excess
over the adapter leftovers. Table for estimation, real data:
TABLE-US-00003 EtOH % Adapter left 0.4x 1.7% 0.5x 2.5% 1.5x 25%
Step D. First Strand cDNA synthesis Take all 13.5 .mu.l of RNA
(eluted in 14 .mu.l of H.sub.2O). Add 1 .mu.l of AR2 RT primer (20
.mu.M stock, 10-50 pmoles). Mix well. Heat the mixture to
70.degree. C. for 2 min and immediately place on ice. Add
master-mix (on ice):
TABLE-US-00004 Affinity-Script RT Mix 1 Reaction 10.times. RT
Buffer 2 .mu.l 100 mMDTT 2 .mu.l 25 mM dNTP Mix 0.8 .mu.l RNAse
inhibitor 0.4 .mu.l Affinity Script RT Enzyme 0.8 .mu.l Total 20
.mu.l
Close stripes, shake in hands, spin 5 sec--put in HOT (55.degree.
C.) incubator. Incubate at 55.degree. C. for 55 min.
Step E. RT primer removal after Reverse Transcription using
ExoSAP-IT. Add 3 .mu.l of ExoSAP-IT into 20 .mu.l of RT reaction
and incubate at 37.degree. C. for 12 min.
Step F. RNA degradation after RT: Add 1 .mu.l of 0.5M EDTA. Add 10%
(2.4 .mu.l) of 1M NaOH. Incubate at 70.degree. C. for 12 minutes.
After this, neutralize with 4.8 .mu.l of 0.5M Acetic Acid.
Step G. cDNA Silane cleanup. Use 12 .mu.l of beads/sample, add some
RLT to the beads, remove all supernatant. Bind with 3.times. volume
of fresh RLT (with beads) and 0.6.times. (RNA+RLT volume) EtOH, mix
well. Wash beads in 123 ul of 70% EtOH twice. Place on magnet and
discard supernatant. Let air-dry at RT for 3-10 minutes.
Add 5.5 .mu.l of H.sub.2O or low TE buffer to the beads (Some water
will evaporate) and keep the sample on the beads.
Step H. Second ligation (ssDNA/ssDNA) 3' Linker Ligation on the
beads
cDNA+adapter--heat at 75.degree. C. for 2 min and put on ice (see
below). Perform reaction as follows:
TABLE-US-00005 Ligation Mix tube cDNA 5 (5.5) 75 C. 3Tr3 adapter,
100 pmoles 1 2 min .fwdarw. ice Add master-mix 10.times. NEB ligase
1 Buffer 2 .mu.l DMSO (100%) 0.8 .mu.l ATP (100 mM) (from
-80.degree. C.) 0.2 .mu.l PEG 8000 (50%) 10 .mu.l T4 RNA Ligase 1,
HiC, 45 Units 1.6 .mu.l Total 20 .mu.l
Mix well pipetting several times, using low-retention tips.
Incubate at 23.degree. C. for 2-4 hours or overnight.
Step I. Ligated cDNA+adapter Silane Linker cleanup. Take extra 5
.mu.l of Silane beads/sample, rinse with RLT, remove supernatant.
Bind with 3.times. volume of fresh RLT and 0.5.times.(RNA+RLT
volume) EtOH, mix well. Wash beads in 123 ul of 70% EtOH twice.
Place on magnet and discard supernatant. Let air-dry at RT for 3-10
minutes. Elute in 27 .mu.l H.sub.2O.
Step J. PCR Enrichment. Make a mix consisting of:
TABLE-US-00006 PCR Mix for 1 Reaction (total of 50 .mu.l): cDNA 23
.mu.l Primer 1 (2P_univ, 25 .mu.M) 1 .mu.l Primer 2 (2P_barcode, 25
.mu.M) 1 .mu.l Phusion or Q5 2.times. MasterMix 25 .mu.l
Run using PCR program:
TABLE-US-00007 98.degree. C. 30 Sec 98.degree. C. 15 sec 67.degree.
C. 30-60 sec .sup. 4 cycles 72.degree. C. 30-60 sec 98.degree. C.
12 sec 72.degree. C. 1 min 6-10 cycles 72.degree. C. 2 min
Use 8-10 cycles if you started from 10-100 ng of poly-A RNA (no
depletion protocol). Use more cycles if you used 50-100 ng of RNA
and depleted rRNAs or used 0.01-5 ng of poly-A RNA or RNA without
depletion.
Step K. SPRI Library cleanup: Use 50 .mu.l of SPRI beads/sample.
Add SPRI beads, mix well many times with slow pipetting. Allow to
sit for 2-15 min. Put on magnet, wait a few minutes. Remove
supernatant. Wash beads twice with 70% Ethanol. Dry beads for 2-5
minutes, elute in 21 .mu.l of H.sub.2O. Load 1 .mu.l on Bioanalyzer
(Agilent) for library analysis and quantification.
Reagents List:
All additives (ATP, DTT, DMSO, dNTPs, etc.) must be stored in
aliquots at -80.degree. C. Non-perishable buffers can be store in a
-25.degree. C. freezer.
10.times.T4 RNA Ligase Reaction Buffer: NEB catalog # B0216B-AS
T4 RNA ligase 1, 3.times. high concentration, 30 U/.mu.L, catalog #
M0204B-AS
RNAse inhibitor, Murine (NEB)
ATP, 100 mM, Roche (Broad SQM) (keep in single-use aliquots at
-80.degree. C.)
PEG8000, 50% in H.sub.2O, Sigma 83271-100ML-F
DMSO HYBRI-MAX, in vials endotoxin free, D2650, Sigma
RLT buffer--Qiagen
RT set:
10.times.RT Buffer from Agilent for AffinityScript
100 mM DTT from Agilent or Affimetrix
dNTPs (25 mM each) from NEB or Agilent
AffinityScript Multiple-Temperature Reverse Transriptase from
Agilent (any RNAseH-minus RT)
RNAse inhibitor, Murine (NEB)
After RT treatments:
ExoSAP-it--Affymetrix
0.5M EDTA, NaOH, Acetic Acid--any ultra-clean.
Example 2
RNA Depletion Protocol
Step A. Oligo-based rRNA depletion after RNA+adapter ligation.
Make your anti-sense RNA probes using both bio-UTP and bio-CTP (1:5
ratio for each=bio-UTP/UTP and bio-CTP/CTP).
Probe generation mix: Total=50 .mu.l: H.sub.2O=22.4 .mu.l, NEB T7
buffer=5 .mu.l
DNA=500-1000 ng=10 .mu.l
100 mM ATP=1 .mu.l, 100 mM GTP=1 .mu.l, 100 mM CTP=0.8 .mu.l
100 mM UTP=0.8 .mu.l, 10 mM bio-UTP=2 .mu.l, 10 mM bio-CTP=2
.mu.l
RNAse inhibitor=1 .mu.l, T7 enzyme mi.times.=4 .mu.l
Incubate 2-15 hours at 37 C. Add TurboDNAse, FastAP, clean with
high-capacity
RNA columns, like RNEasy (Qiagen).
Step B. Oligo-based rRNA depletion Hybridization. Use 10.times.rRNA
probes mix (18s+28s+5.8s+5s+other regulatory
RNAs=1.times.+2.35.times.+0.25.times.+0.2.times.+0.2.times.) with
your sample (500 ng of rRNA probe mix for 50 ng of input):
TABLE-US-00008 # ratio .mu.g .mu.l conc m18s 1.2 12 20 0.6
m28s.sub.1 2.9 29 66 0.44 28sL 0.3 3 6 0.5 5.8s 0.3 3 8 0.36 5s 0.2
2 3.3 0.6 45s 0.31 3 7.2 0.43 rRNA spacers 0.31 3 7.4 0.42 U3B 0.21
2.1 4.5 0.47 U1B 0.1 1 1.7 0.59 U3A 0.1 1 2.2 0.45 U2 0.1 1 2.3
0.44 U5 0.05 0.5 2 0.24 H.sub.2O = 173 60.7 130.6 200 ng/.mu.L
Hybridize in large tubes. Heat Denature RNA+probes at 72.degree. C.
for 2 min.
TABLE-US-00009 RNA probe mix (500 ng) 2 .mu.l 2.times. Hyb Buffer
(heated to 72.degree. C.) 25 .mu.l Ligated RNA + Adapter (100 ng)
23 .mu.l Total 50 .mu.l
Bind at 70.degree. C. for 40 min in ThermoMixer with shaking
Prepare Streptavidin Beads after 30 minutes of incubation. Mix
beads well, take 12 .mu.l of Streptavidin beads per pool (around 40
.mu.l/4 .mu.g of used rRNA probes.). Place beads on magnet, remove
supernatant. Wash the beads in 50 .mu.l of 1.times. Hybridization
Buffer. Wash beads in 100 .mu.l of solution A for 2 min. Wash beads
in 100 .mu.l of solution B. Wash beads in 100 .mu.l of 1.times.
Hybridization Buffer. Repeat a few times. Resuspend beads in 10
.mu.l of 1.times. Hybridization Buffer using shaking ThermoMixer
(70.degree. C.).
Probe removal (Bind Hybrids to beads): Add all of hot (70.degree.
C.) Streptavidin Beads to hybridization reaction. Incubate at
68.degree. C. for 15 min on ThermoMixer. Quickly place on the
magnet and quickly transfer ALL Supernatant (which contains rRNA
depleted sample) to fresh tube.
Silane sample cleanup of rRNA depleted sample: Take 20 .mu.l of
Silane beads/sample, add some RLT, remove all supernatant from the
beads. Bind with 3.times. volume of fresh RLT and 1.times.(RNA+RLT)
volume of EtOH, mix well. Wash beads in 123 ul of 70% EtOH twice
out of magnet, Place on magnet and discard supernatant. Let air-dry
at RT for 3-10 minutes. Elute depleted sample from beads using
water
rRNA depletion hybridization buffer:
TABLE-US-00010 1.times. LiCl Lysis Buffer Final (M or %) Stock (M
or %) 1.times. (mL) 20 mM Tris-HCl (pH 7.5) 0.02 1M 0.2 5 mM EDTA
0.005 0.5M.sup. 0.1 500 mM LiCl 0.5 8M 0.625 0.25% Triton X-100
0.25% 10% 0.25 0.1% SDS 0.1 20% 0.05 0.1% Na-Deoxycholate 0 4 0
H.sub.2O up to 10 ml total 10 ml
In view of the many possible embodiments to which the principles of
our invention may be applied, it should be recognized that
illustrated embodiments are only examples of the invention and
should not be considered a limitation on the scope of the
invention. Rather, the scope of the invention is defined by the
following claims. The disclosed method is defined by the following
claims as our invention and all that comes within the scope and
spirit of this disclosure.
* * * * *